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Dr. Florence Schubotz


Organic Geochemistry


+49 421 218-65724


+49 421 218-65715



MARUM Pavillon

Florence Schubotz

I'm a senior scientist affiliated to the Organic Geochemistry group of Kai-Uwe Hinrichs.
I can also be reached with this email adress: [Bitte aktivieren Sie Javascript]

Photo: Harald Rehling

Research Interests

I'm an organic geochemist studying the interactions of microorganisms with their surrounding environment. The number of metabolic reactions microbes can perform are vast and so are the types of habitats they can live in. I am particularly interested in studying microbial communities that live in extreme environments, such as the Earth'*s crust, hot springs, cold seeps, hypersaline lakes and the oligotrophic ocean. My main line of research lies in investigating microbial physiological response to environmental change, but also how microorganisms shape and modify their surrounding environment.
To investigate the microbial ecophysiology I use the taxonomic, metabolic and physiologic information encoded in cellular membrane lipids. Together with the analyses of metabolites and other organic molecules I gain insights on the role microbes play in the flow and fate of organic matter in ecosystems.

Research Projects

Life in extreme environments: Adaptations and microbial community dynamics in hydrothermal systems, crustal rocks and the deep biosphere
Collaborators: Frieder Klein (WHOI, USA), Virginia Edgcomb (WHOI, USA), Jason Sylvan (TAMU, USA), William Orsi (LMU, Germany)

Some of the most challenging environments for life are found within deeply buried sediments and basement rocks, where temperatures and pressures are high and pore space and water availability are low. Such sites also serve as comparative models for conditions that have prevailed throughout Earth‟s history and thus may provide windows into the early evolution of life on Earth and elsewhere. We are using a combination of intact polar membrane lipid analysis and molecular biological tools to characterize physiological adaptations and metabolic capacities of microbial communities in these unique microbial habitats.

Asphalt volcanism in the southern Gulf of Mexico: Biotic and abiotic processes involved in oil degradation
Collaborators: Gerhard Bohrmann (Uni-Bremen, Germany), Gunter Wegener (MPI Bremen, Germany), Gregory Ventura (SMU, Canada), Elva Escobar (UNAM, Mexico)

Oil pollution and the persistence of hydrocarbons in the marine environment is of high ecological significance and greatly depends on the composition of the respective oil. Naturally occuring hydrocarbon seeps provide a unique chance to study long-term compositional changes of oil in the marine evironment and its effects on ecosystems. Deposits of heavy oil and asphalt in the southern Gulf of Mexico forms the basis of a natural ecosystem with a thriving cold seep community including tube worms, mussels, sea cucumbers and crabs. With this project I seek to unfold postdepositional mechanisms involved in the biotic and abiotic degradation of heavy oils and test the efficient recycling of petroleum compounds by microorganisms. Insights into these processes can aid future mitigations of oil spills.

Oil slick sampling in the Gulf of Mexico during Exp. M114
DV Chikyu
Gas sampling during IODP Exp. 370
Rock sample from IODP Exp. 360
Gas sampling during IODP Exp. 370
Gulf of Mexico, M114

Seafloor image: Copyright MARUM

Photo: Christian Rohleder

Survival of the fittest: Unraveling the role of membrane lipids in physiological adaptations of marine bacteria
Collaborators: Tanja Bosak (MIT, USA), Otto Geiger (CCG and UNAM, Mexico)

With this project I intend to shed light into physiological response mechanisms of marine bacteria by investigating modifications of their membrane lipids under environmental stress. Cellular membrane lipids are vital components that help cells acclimate to changing environmental conditions. In the ocean, membrane lipid changes have been reported with temperature, salinity and nutrient limitation. In particular aminolipids, such as betaine and ornithine lipids, have been shown to be sensitive to environmental stress. Despite being major lipids in the ocean, their biological sources are in many cases still unknown. With my research I want to exploit the vast potential these compounds harbor as ecological markers. My goal is to combine targeted genetic and lipid-based techniques to identify sources and functions of aminolipids and other polar lipids in the marine environment.

Oil slick sampling in the Gulf of Mexico, M114
Oxygen measurements during asphalt incubations

Curriculum Vitae

2022 9 months maternity leave
since 2021 Senior Scientist, tenured, MARUM, University of Bremen
2019-2021 Own Position (DFG Priority Program 527, IODP), MARUM, University of Bremen
2018-2019 8 months maternity leave
2014-2018 Independent Postdoc (Central Research Development Funds), University of Bremen & MARUM
2013-2014 Research Associate, MIT, USA
2011-2013 Research Fellow (Feodor-Lynen Fellowship, Alexander von Humboldt Society), MIT, USA
2009-2010 PostDoc, MARUM & University of Bremen
2009 PhD, University of Bremen
2006-2009 PhD candidate, Advisor K-U Hinrichs
2007-2009 Member of international graduate school GLOMAR
2005 M.Sc., University of Bremen
2002 Vordiplom, Carl-von-Ossietzly University Oldenburg
2002-2003 ERASMUS at Universidad the Las Palmas de Gran Canaria, Spain

Publications (peer-reviewed)

2024 Mills J, Gebhard LJ, Schubotz F, Shevchenko A, Speth D, Liao Y, Duggin I, Marchfelder A, Erdmann S Extracellular vesicles of Euryarchaeota: precursor to eukaryotic membrane trafficking (2024) Proceedings of the National Academy of Sciences of the United States. Doi:10.1073/pnas.2311321121.
Achberger A, Jones R, Jamieson J, Holmes II CP, Schubotz F, Meyer NR, Dekas AE, Moriarty S, Reeves EP, Manthey A, Brünjes J, Fornari DJ, Tivey MK, Toner BM, Sylvan JB (2024) Inactive Hydrothermal Vent Deposits are Important Sites for Primary Productivity in the Deep Ocean. Nature Microbiology. doi.org/10.1038/s41564-024-01599-9
2023 Ruben M, Hefter J, Schubotz F, Geibert W, Butzin M, Gentz T, Grotheer H, Forwick M, Szcuci´nski W, Mollenhauer G (2023) Fossil organic carbon utilization in marine Arctic fjord sediments. Nature Geosciences, 16:625-630. doi.org/10.1038/s41561-023-01198-z
2022 Rolli E, Marasco R, Fusi M, Scaglia B, Schubotz F, Mapelli F, Ciccazzo S, Brusetti L, Trombino L, Tambone F., Adani F., Borin S, Daffonchio D Environmental micro-niche filtering shapes bacterial pioneer communities during primary colonization of a Himalayas’ glacier forefield. Accepted Environmental Microbiology, October 2022.

Schubotz F, Septhon, MA, Derenne S (2022) Biomarkers in extreme environments on Earth and the search for extraterrestrial life in our Solar System. Elements 18:100-106.

*Brünjes J, Seidel M, Gan S, Song M, Dittmar T, Schubotz F (2022) Natural asphalt seeps are potential sources for recalcitrant oceanic dissolved organic sulfur and dissolved black carbon. Environmental Science and Technology. doi.org/10.1021/acs.est.2c01123


Song M, Schubotz F, Kellermann MY, Hansen CT, Bach W, Teske AP, Hinrichs K-U (2021) Non-methane hydrocarbon gases formed by reduction of volatile fatty acids. Proceedings of the National Academy of Sciences of the United States, 118, e2005219118. doi.org/10.1073/pnas.2005219118

Kars, M, Köster, M, Henkel S, Stein R, Schubotz F, Xiang Zhao X, Bowden S, Roberts AP, Kazuto Kodama K (2021) Influence of Early Low-Temperature and Later High-Temperature Diagenesis on Magnetic Mineral Assemblages in Marine Sediments from the Nankai Trough Geochemistry, Geophysics, Geosystems, 22, e2021GC010133. doi.org/10.1029/2021GC010133

Coskun ÖK, Vuillemin A, Schubotz F, Klein F, Sichel ES, Eisenreich, W, Orsi WD (2021) Quantifying the effects of hydrogen on carbon assimilation in a seafloor microbial community associated with ultramafic rocks. ISME Journal. https://doi.org/10.1038/s41396-021-01066-x

Köster, M, Kars, MAC, Schubotz, F, Tsang, M-Y, Morono, Y, Inagaki, F, Heuer, VB, Kasten, S, Susann Henkel (2021) Evolution of (bio-)geochemical processes and diagenetic alteration of sediments along the tectonic migration of ocean floor in the Shikoku Basin off Japan. Geochemistry, Geophysics, Geosystems, 22, e2020GC009585. doi: 10.1029/2020GC009585


Heuer VB, Inagaki F, Morono Y, Kubo Y, Maeda L, Spivack A, Viehweger B, Treude T, Beulig F, Schubotz F, Tonai S, Bowden S, Cramm M, Henkel S, Hirose T, Homola K, Hoshino T, Ijiri A, Imachi H, Kamiya N, Kaneko M, Lagostina L, Manners H, McClelland H-L, Metcalfe K, Okutsu N, Pan D, Raudsepp MJ, Sauvage J, Tsang M-Y, Wang DT, Whitaker E, Yamamoto Y, Yang K, Adhikari RR, Glombitza C, Kallmeyer J, Wendt J, Wörmer L, Yamada Y, Kinoshita K, Hinrichs K-U (2020) Temperature limits to deep subseafloor life in the Nankai Trough subduction zone. Science, 370:1230-1234. doi: 10.1126/science.abd7934

Quemener M, Mara P, Schubotz F, Beaudoin D, Wei L, Wee S-Y, Sylvan J, Barbier G, Edgcomb V, Burgaud G (2020) Meta-Omics highlights the diversity, activity and adaptation of fungi in deep oceanic crust Eviron. Microbiol., 22(9):3950-3967. doi: 10.1111/1462-2920.15181

Wörmer L, Gajendra N, Schubotz F, Matys E, Evans T, Summons RE, Hinrichs, K-U (2020) A micrometer snapshot on chlorophototroph spatial distribution: Mass Spectrometry Imaging of microbial mats in the geothermal Octopus Spring (Yellowstone National Park). Geobiology, 18(6):742-759. doi.org/10.1111/gbi.12411

Wagner S, Schubotz F, Kaiser K, Hallmann C., Waska H., Rossel PE, Hansman R, Elvert M, Middelburg JJ, Engel A, Blattmann T, Catalá TS, Lennartz ST, Gomez-Saez GV, Pantoja-Gutiérrez S, Rui Bao, Valier Galy (2020) Soothsaying DOM: A current perspective on the future of oceanic dissolved organic carbon. Frontiers in Marine Science 7:341. doi: 10.3389/fmars.2020.00341

Li J, Mara P, Schubotz F, Sylvan J, Burgaud G, Klein F, Beaudoin D, Wee S-Y, Dick H, Lott S, Cox R, Meyer LAE, Quémener M, Blackman DK, Edgcomb VP (2020) Recycling and metabolic flexibility dictate life in the lower oceanic crust. Nature, 579:250-255. doi.org/10.1038/s41586-020-2075-5

Boyer G, Schubotz F, Summons RE, Woods J, Shock E (2020) Carbon oxidation state in microbial polar lipids suggests adaptation to hot spring temperature and redox gradients. Frontiers in Microbiology. 11:229. doi:10.3389/fmicb.2020.00229.
Tsang M-Y, Bowden S, Mohammed AY, Wen Z, Tonai S, Muirhead DK, Yang K, Yamamoto Y, Kamiya N, Okutsu N, Hirose T, Kars M, Schubotz F, Ijiri A, Morono Y, Inagaki F, Heuer V, Hinrichs K-U (2020) Hot fluids, burial metamorphism and thermal histories in the underthrust sediments at IODP 370 Site C0023, Nankai Accretionary complex. Marine and Petroleum Geology 112:104080. doi.org/10.1016/j.marpetgeo.2019.104080
2019 Laso-Pérez R, Hahn C, van Vliet Daan M, Tegetmeyer HE, Schubotz F, Smit NT, Pape T, Sahling H, Bohrmann G, Boetius A, Knittel K, Wegener G (2019) Anaerobic degradation of non-methane alkanes by ‘Candidatus Methanoliparia’ in hydrocarbon seeps of the Gulf of Mexico. mBio 10:e01814-19. doi.org/10.1128/mBio.01814-19
Glabonjat RA, Raber G, Jensen KB, Schubotz F, Boyd ES, Francesconi K (2019) Arsenolipids in sediments from the Great Salt Lake. Environmental Chemistry 16:303-311. doi.org/10.1071/EN19135
Zhuang G-C, Montgomery A, Song M, Liu J, Schubotz F, Teske A, Hinrichs K-U, Joye SB. Generation and utilization of volatile fatty acids and alcohols in hydrothermally altered sediments of the Guaymas Basin. Geophysical Research Letters, 46:2637-2646. doi.org/10.1029/2018GL081284

Imachi H, Tasumi E, Takaki Y, Hoshino T, Schubotz F, Gan S, Tu T-H, Saito Y, Yamanaka Y, Ijiri A, Matsui Y, Morono Y, Takai K, Hinrichs K-U, Inagaki F (2019) Cultivable microbial community in 2-km-deep, 20-million-year-old subseafloor coalbeds through ~1000 days anaerobic bioreactor cultivation. Scientific Reports, 9:2305. doi.org/10.1038/s41598-019-38754-w

2018 Schubotz, F., Xie, S., Lipp J.S., Hinrichs, K.-U., Wakeham, S. Diversity of intact polar lipids in the oxygen minium zone of the Eastern Tropical North Pacific: Biogeochemical implications of non-phosphorus lipids (2018) Biogeosciences, 15:6481-6501. doi.org/10.5194/bg-15-6481-2018

Hamada Y, Hirose T, Ijiri A, Yamada Y, Sanada Y, Saito S, Sakurai N, Sugihara T, Yokoyama T, Saruhashi T, Hoshino T, Kamiya N, Bowden S, Cramm M, Henkel S, Homola K, Imachi H, Kaneko M., Lagostina L, Manners H, McClelland H-L, Metcalfe K, Okutsu N, Pan D, Raudsepp MJ, Sauvage J, Schubotz F, Spivack A, Tonai S, Treude T, Tsang M-Y, Viehweger B, Wang DT, Whitaker E, Yamamoto Y, Yang K, Kinoshita M, Maeda L, Kubo Y, Morono Y, Inagaki F, Heuer VB (2018) In-situ mechanical weakness of subducting sediments beneath a plate boundary décollement in the Nankai Trough Progress in Earth and Planetary Science 5:70.

Carr, S., Schubotz, F., Dunbar, R., Mills C., Dias, R.R., Summons, R.E., Mandernack, K. (2018) Acetoclastic Methanosaeta are dominant methanogens in organic-rich Antarctic marine sediments. The ISME Journal 12:330-342.
2016 Sahling, H., Rubin Blum, M., Borowski, C., Escobar-Briones, E., Gaytán-Caballero, A., Hsu, C.-W., Loher, M., McDonald, I., Marcon, Y., Pape, T., Römer, M., Schubotz, F., Smrzka, D., Wegener, G., Bohrmann, G. (2016) Seafloor observations at Campeche Knolls, southern Gulf of Mexico: coexistance of asphalt deposits, oil seepage and gas venting. Biogeosciences 13:4491-4512
Bosak, T., Schubotz F., Santiago-Torio, A., Kuehl, J., Carlson, H.K., Summons, R.E., Arkin, A.P., Deutschbauer, A.M. (2016) System-wide adaptations of Desulfovibrio alaskensis G20 to phosphate-limited conditions. PLoS ONE 11(12): e0168719. doi.org/10.1371/journal.pone.0168719
2015 Klein, F., Humphris, S.E., Guo W., Schubotz, F., Schwarzenbach, E.M., Orsi, E.D. (2015) Fluid Mixing and the deep biosphere of a fossil Lost City-type hydrothermal system at the Iberia Margin. Proceedings of the National Academy of Sciences, 112:12036-12041. doi:10.1073/pnas.1504674112
Segarra, K.E.A., Schubotz, F., Samarkin, V., Yoshinaga, M.Y., Hinrichs, K.-U., Joye, S.B. (2015) Anaerobic oxidation of methane reduces methane fluxes from freshwater wetlands. Nature Communications, 6:7477. doi:10.1038/ncomms8477
Escobedo-Hinojosa, W.I., Vences-Guzmán, M.A., Schubotz, F., Sandoval-Calderón, M., Summons, R.E., López-Lara, I.M., Geiger, O., Sohlenkamp, C. (2015) OlsG (Sinac_1600) is an ornithine lipid N-methyltransferase from the planctomycete Singulisphaera acidiphila. Journal of Biological Chemistry, 290:15102-15111. doi: 10.1074/jbc.M115.639575
Schubotz, F., Hays, L.E., Meyer-Dombard, D.R., Gillespie, A., Shock, E., Summons, R. (2015) Stable isotope labeling confirms mixotrophic nature of streamer biofilm communities at alkaline hot springs. Frontiers in Microbiology, 6:42. doi:10.3389/fmicb.2015.00042
2014 Biller, S., Schubotz, F., Roggensack, S., Thompson, A., Summons, R., Chisholm, S.W. (2014) Bacterial vesicles in marine ecosystems. Science 343, 183-186
Xie, S., Liu, X.-L., Schubotz, F., Wakeham, S.G., Hinrichs, K.-U. (2014) Distribution of glycerol ether lipids in the oxygen minimum zone of the Eastern Tropical North Pacific Ocean. Organic Geochemistry 71, 60-71.
2013 Edgcomb V.P., Bernhard J.M., Beaudoin D., Pruss S., Welander P.V., Schubotz F., Mehay S., Gillespie A.L., Summons R.E. (2013) Molecular indicators of microbial diversity in oolitic sands of Highborne Cay, Bahamas. Geobiology 11, 234-251.
Raggi, L., Schubotz, F., Hinrichs, K.-U., Dubilier, N., Petersen, J.M. Bacterial symbionts of Bathymodiolus mussels and Escarpia tubeworms from Chapopote, an asphalt seep in the southern Gulf of Mexico. (2013) Environmental Microbiology 15, 1969-1987.
Schubotz F., Meyer-Dombard D.R., Bradley A.S., Fredricks H.F., Hinrichs K.-U., Shock E.L., Summons R.E. (2013) Spatial and temporal variability of biomarkers and microbial diversity reveal metabolic and community flexibility in streamer biofilm communities in the Lower Geyser Basin, Yellowstone National Park. Geobiology 11, 549-569.
2012 Bühring, S.I., Schubotz, F., Harms, C., Lipp, J.S., Amils, R. and Hinrichs, K.-U. (2012) Lipid signatures of acidophilic microbial communities in an extreme, acidic environment: Río Tinto, Spain. Organic Geochemistry 47, 66-77.
Kellermann, M.Y., Schubotz, F., Elvert, M., Lipp, J.S., Birgel D., Prieto Mollar, X., Dubilier N., Hinrichs, K.-U. (2012) Symbiont-host relationships in chemosynthetic mussels: A comprehensive lipid biomarker study. Organic Geochemistry 43, 112-124.
Wakeham, S.G., Turich, C., Schubotz, F., Podlaska, A., Li, X.N., Varela, R., Astor, Y., Sáenz, J.P., Rush, D., Sinninghe Damsté, J.S., Summons, R.E., Scranton, M.I., Taylor, G.T. and Hinrichs, K.-U. (2012) Biomarkers, Chemistry and Microbiology Show Chemoautotrophy in a Multilayer Chemocline in the Cariaco Basin. Deep Sea Research I 63, 133-156.
2011 Schubotz, F., Lipp, J.S., Elvert and Hinrichs K.-U. (2011) Stable carbon isotopic composition of intact polar lipids reveal complex carbon flow patterns among hydrocarbon degrading microbial communities at the Chapopote asphalt volcano. Geochimica et Cosmochimica Acta 75, 4377-4398.
Schubotz, F., Lipp, J.S., Elvert, M., Kasten, S., Prieto-Mollar, X., Zabel, M., Bohrmann, G. and Hinrichs K.-U. (2011) Petroleum degradation and associated microbial signatures at the Chapopote asphalt volcano, Southern Gulf of Mexico. Geochimica et Cosmochimica Acta 75, 4399-4415.
Yoshinaga M.Y., Kellermann M.Y, Rossel P.E., Schubotz F., Lipp J.S., Hinrichs, K.-U. (2011) Systematic fragmentation patterns of archaeal intact polar lipids by high-performance liquid chromatography/electrospray ionization ion-trap mass spectrometry. Rapid Communications in Mass Spectrometry 25, 1-12.
2010 Borin, S., Ventura, S., Tambone, F., Mapelli, F., Schubotz, F., Brusetti, L., Scaglia, B., D’Acqui, L., Solheim, B., Turicchia, S., Hinrichs, K.-U., Baldi, F., Adani, F. and Daffonchio, D. (2010) Rock weathering creates oases of life in a high arctic desert. Environmental Microbiology 2, 293-303.
Lichtschlag, A., Felden, J., Wenzhöfer, F., Schubotz, F., Ertefai, T., Boetius, A. and deBeer, D. (2010) Methane and sulfide fluxes in permanent anoxia: in situ studies at the Dvurechenskii mud volcano (Sorokin Through, Black Sea). Geochimica et Cosmochimica Acta 74, 5002-5018.
Rethemeyer, J., Schubotz, F., Talbot, H.M., Cooke, M.P., Hinrichs, K.-U. and Mollenhauer, G. (2010) Distribution of polar membrane lipids in permafrost soils and sediments of a small Arctic catchment. Organic Geochemistry 41, 1130-1145. 

2009 Schubotz, F., Wakeham, S.G., Lipp, J.S., Fredricks, H.F. and Hinrichs, K.-U. (2009) Detection of microbial biomass by intact polar membrane lipid analysis in the water column and surface sediments of the Black Sea. Environmental Microbiology 11(10), 2720-2734. 

2008 Strapoc, D., Picardal, F.W., Turich, C., Schaperdoth, I., Macalady, J.L., Lipp, J.S., Lin, Y.-S., Ertefai, T.F., Schubotz, F., Hinrichs, K.-U., Mastalerz, M. and Schimmelmann, A. (2008) An analysis of the methane-producing microbial community in a coal bed of the Illinois Basin. Applied and Environmental Microbiology 74(8), 2424-2432.

Book Chapters

Wegener, G., Knittel, K., Bohrmann, G., Schubotz, F. Asphaltic hydrocarbon emission at the Chapopote Knoll, Gulf of Mexico (2020) In: A. Teske and V. Carvalho (eds) Marine Hydrocarbon Seeps, Springer Oceanogaphy. Springer Nature Switzerland.

Schubotz, F. (2019) Membrane Homeostasis upon Nutrient (C, N, P) Limitation. In: Geiger O. (eds) Biogenesis of Fatty Acids, Lipids and Membranes. Handbook of Hydrocarbon and Lipid Microbiology. Springer Cham.